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Showing metabocard for Pentanal (HMDB0031206)

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Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2012-09-11 17:41:37 UTC
Update Date2023-02-21 17:20:02 UTC
HMDB IDHMDB0031206
Secondary Accession Numbers
  • HMDB31206
Metabolite Identification
Common NamePentanal
DescriptionPentanal, also known as N-valeraldehyde or amyl aldehyde, belongs to the class of organic compounds known as alpha-hydro gen aldehydes. These are aldehydes with the general formula HC(H)(R)C(=O)H, where R is an organyl group. Pentanal is a saturated fatty aldehyde composed from five carbons in a straight chain. Thus, pentanal is considered to be a fatty aldehyde lipid molecule. Pentanal is a very hydrophobic molecule, practically insoluble in water, and relatively neutral. Pentanal is an almond, berry, and bready tasting compound. Pentanal is found, on average, in the highest concentration within a few different foods, such as black walnuts, milk (cow), and carrots and in a lower concentration in corns, tortilla, and safflowers. Pentanal has also been detected, but not quantified, in several different foods, such as crustaceans, garden tomato, herbs and spices, and guava. This could make pentanal a potential biomarker for the consumption of these foods.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0031206 (Pentanal)

  Mrv1652309272007352D          

  6  5  0  0  0  0            999 V2000
   -0.1914    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1269    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9519    1.1269    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1269    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
M  END
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3D MOL for HMDB0031206 (Pentanal)

HMDB0031206
     RDKit          3D
Pentanal
 16 15  0  0  0  0  0  0  0  0999 V2000
   -1.7754    0.3813    0.0361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7593   -0.5306   -0.6449 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2738   -0.9770    0.3404 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0460    0.1318    0.9632 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7915    0.9454   -0.0369 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7782    0.7311   -1.2240 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1958    1.2369    0.4366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4722    0.7355   -0.7367 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2788   -0.2146    0.8220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3603   -1.4360   -0.9548 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3807   -0.0787   -1.5611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2753   -1.5077    1.1630 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9789   -1.6933   -0.1006 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4289    0.7935    1.6155 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8223   -0.2960    1.6436 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3782    1.7785    0.3395 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
M  END
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3D SDF for HMDB0031206 (Pentanal)

  Mrv1652309272007352D          

  6  5  0  0  0  0            999 V2000
   -0.1914    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1269    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9519    1.1269    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7144    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1269    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0031206

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCC=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O/c1-2-3-4-5-6/h5H,2-4H2,1H3

> <INCHI_KEY>
HGBOYTHUEUWSSQ-UHFFFAOYSA-N

> <FORMULA>
C5H10O

> <MOLECULAR_WEIGHT>
86.1323

> <EXACT_MASS>
86.073164942

> <JCHEM_ACCEPTOR_COUNT>
1

> <JCHEM_ATOM_COUNT>
16

> <JCHEM_AVERAGE_POLARIZABILITY>
10.321567480039405

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
pentanal

> <ALOGPS_LOGP>
1.41

> <JCHEM_LOGP>
1.2077112103333332

> <ALOGPS_LOGS>
-0.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
17.823955584289568

> <JCHEM_PKA_STRONGEST_BASIC>
-6.944302342827888

> <JCHEM_POLAR_SURFACE_AREA>
17.07

> <JCHEM_REFRACTIVITY>
25.5472

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.48e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
pentanal

> <JCHEM_VEBER_RULE>
1

$$$$
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3D-SDF for HMDB0031206 (Pentanal)

HMDB0031206
     RDKit          3D
Pentanal
 16 15  0  0  0  0  0  0  0  0999 V2000
   -1.7754    0.3813    0.0361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7593   -0.5306   -0.6449 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2738   -0.9770    0.3404 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0460    0.1318    0.9632 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7915    0.9454   -0.0369 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7782    0.7311   -1.2240 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1958    1.2369    0.4366 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4722    0.7355   -0.7367 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2788   -0.2146    0.8220 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3603   -1.4360   -0.9548 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3807   -0.0787   -1.5611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2753   -1.5077    1.1630 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9789   -1.6933   -0.1006 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4289    0.7935    1.6155 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8223   -0.2960    1.6436 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3782    1.7785    0.3395 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  2  0
  1  7  1  0
  1  8  1  0
  1  9  1  0
  2 10  1  0
  2 11  1  0
  3 12  1  0
  3 13  1  0
  4 14  1  0
  4 15  1  0
  5 16  1  0
M  END
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PDB for HMDB0031206 (Pentanal)

HEADER    PROTEIN                                 27-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   27-SEP-20         0                                  
HETATM    1  C   UNK     0      -0.357   1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       6.311   2.104   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5                                                            
MASTER        0    0    0    0    0    0    0    0    6    0   10    0
END
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3D PDB for HMDB0031206 (Pentanal)

COMPND    HMDB0031206
HETATM    1  C1  UNL     1      -1.775   0.381   0.036  1.00  0.00           C  
HETATM    2  C2  UNL     1      -0.759  -0.531  -0.645  1.00  0.00           C  
HETATM    3  C3  UNL     1       0.274  -0.977   0.340  1.00  0.00           C  
HETATM    4  C4  UNL     1       1.046   0.132   0.963  1.00  0.00           C  
HETATM    5  C5  UNL     1       1.792   0.945  -0.037  1.00  0.00           C  
HETATM    6  O1  UNL     1       1.778   0.731  -1.224  1.00  0.00           O  
HETATM    7  H1  UNL     1      -1.196   1.237   0.437  1.00  0.00           H  
HETATM    8  H2  UNL     1      -2.472   0.735  -0.737  1.00  0.00           H  
HETATM    9  H3  UNL     1      -2.279  -0.215   0.822  1.00  0.00           H  
HETATM   10  H4  UNL     1      -1.360  -1.436  -0.955  1.00  0.00           H  
HETATM   11  H5  UNL     1      -0.381  -0.079  -1.561  1.00  0.00           H  
HETATM   12  H6  UNL     1      -0.275  -1.508   1.163  1.00  0.00           H  
HETATM   13  H7  UNL     1       0.979  -1.693  -0.101  1.00  0.00           H  
HETATM   14  H8  UNL     1       0.429   0.793   1.616  1.00  0.00           H  
HETATM   15  H9  UNL     1       1.822  -0.296   1.644  1.00  0.00           H  
HETATM   16  H10 UNL     1       2.378   1.779   0.339  1.00  0.00           H  
CONECT    1    2    7    8    9
CONECT    2    3   10   11
CONECT    3    4   12   13
CONECT    4    5   14   15
CONECT    5    6    6   16
END
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SMILES for HMDB0031206 (Pentanal)

CCCCC=O
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INCHI for HMDB0031206 (Pentanal)

InChI=1S/C5H10O/c1-2-3-4-5-6/h5H,2-4H2,1H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
Chemical FormulaC5H10O
Average Molecular Weight86.1323
Monoisotopic Molecular Weight86.073164942
IUPAC Namepentanal
Traditional Namepentanal
CAS Registry Number110-62-3
SMILES
CCCCC=O
InChI Identifier
InChI=1S/C5H10O/c1-2-3-4-5-6/h5H,2-4H2,1H3
InChI KeyHGBOYTHUEUWSSQ-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as alpha-hydrogen aldehydes. These are aldehydes with the general formula HC(H)(R)C(=O)H, where R is an organyl group.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbonyl compounds
Direct ParentAlpha-hydrogen aldehydes
Alternative Parents
Substituents
  • Alpha-hydrogen aldehyde
  • Organic oxide
  • Hydrocarbon derivative
  • Short-chain aldehyde
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Ontology
Physiological effect
Organoleptic effect
Disposition
Biological locationRoute of exposureSource
ProcessNot Available
Role
Industrial application
Physical Properties
StateLiquid
Experimental Molecular Properties
PropertyValueReference
Melting Point-92 °CNot Available
Boiling Point102.00 to 103.00 °C. @ 760.00 mm HgThe Good Scents Company Information System
Water Solubility11.7 mg/mL at 25 °CNot Available
LogP1.423 (est)The Good Scents Company Information System
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
Biospecimen Locations
  • Feces
  • Saliva
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Both
Normal		 details
FecesDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
FecesDetected but not QuantifiedNot QuantifiedNewborn (0-30 days old)Both
Normal		 details
SalivaDetected but not QuantifiedNot QuantifiedAdult (>18 years old)Not SpecifiedNormal details
Abnormal Concentrations
Associated Disorders and Diseases
Disease References
Ulcerative colitis
  1. Garner CE, Smith S, de Lacy Costello B, White P, Spencer R, Probert CS, Ratcliffe NM: Volatile organic compounds from feces and their potential for diagnosis of gastrointestinal disease. FASEB J. 2007 Jun;21(8):1675-88. Epub 2007 Feb 21. [PubMed:17314143 ]
  2. Ahmed I, Greenwood R, Costello B, Ratcliffe N, Probert CS: Investigation of faecal volatile organic metabolites as novel diagnostic biomarkers in inflammatory bowel disease. Aliment Pharmacol Ther. 2016 Mar;43(5):596-611. doi: 10.1111/apt.13522. Epub 2016 Jan 25. [PubMed:26806034 ]
Nonalcoholic fatty liver disease
  1. Raman M, Ahmed I, Gillevet PM, Probert CS, Ratcliffe NM, Smith S, Greenwood R, Sikaroodi M, Lam V, Crotty P, Bailey J, Myers RP, Rioux KP: Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease. Clin Gastroenterol Hepatol. 2013 Jul;11(7):868-75.e1-3. doi: 10.1016/j.cgh.2013.02.015. Epub 2013 Feb 27. [PubMed:23454028 ]
Crohn's disease
  1. Ahmed I, Greenwood R, Costello Bde L, Ratcliffe NM, Probert CS: An investigation of fecal volatile organic metabolites in irritable bowel syndrome. PLoS One. 2013;8(3):e58204. doi: 10.1371/journal.pone.0058204. Epub 2013 Mar 13. [PubMed:23516449 ]
  2. Ahmed I, Greenwood R, Costello B, Ratcliffe N, Probert CS: Investigation of faecal volatile organic metabolites as novel diagnostic biomarkers in inflammatory bowel disease. Aliment Pharmacol Ther. 2016 Mar;43(5):596-611. doi: 10.1111/apt.13522. Epub 2016 Jan 25. [PubMed:26806034 ]
Associated OMIM IDs
DrugBank IDDB01919
Phenol Explorer Compound IDNot Available
FooDB IDFDB003228
KNApSAcK IDC00007400
Chemspider ID7772
KEGG Compound IDNot Available
BioCyc IDCPD-9053
BiGG IDNot Available
Wikipedia LinkPentanal
METLIN IDNot Available
PubChem Compound8063
PDB IDPTL
ChEBI ID84069
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDrw1009331
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .

Enzymes

Enzyme Details
1. cAMP-dependent protein kinase catalytic subunit alpha
General function:
Involved in protein serine/threonine kinase activity
Specific function:
Phosphorylates a large number of substrates in the cytoplasm and the nucleus
Gene Name:
PRKACA
Uniprot ID:
P17612
Molecular weight:
40589.4
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [PubMed:17139284 ]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [PubMed:17016423 ]
  3. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [PubMed:10592235 ]